Microbiome Diversity in the Bronchial Tracts of Patients with Chronic Obstructive Pulmonary Disease

Abstract

i Culture of bacteria from bronchial secretions in respiratory patients has low sensitivity and does not allow for complete assessment of microbial diversity across different bronchial compartments. In addition, a significant number of clinical studies are based on sputum samples, and it is not known to what extent they describe the real diversity of the mucosa. In order to identify previously unrecognized lower airway bacteria and to investigate the complexity and distribution of microbiota in patients with chronic obstructive pulmonary disease (COPD), we performed PCR amplification and pyrosequencing of the 16S rRNA gene in patients not showing signs or symptoms of infection. Four types of respiratory samples (sputum, bronchial aspirate, bronchoalveolar lavage, and bronchial mucosa) were taken from each individual, obtaining on average >1,000 16S rRNA sequences per sample. The total number of genera per patient was >100, showing a high diversity, with Streptococcus, Prevotella, Moraxella, Haemophilus, Acinetobacter, Fusobacterium, and Neisseria being the most commonly identified. Sputum samples showed significantly lower diversity than the other three sample types. Lower-bronchial-tree samples, i.e., bronchoalveolar lavage and bronchial mucosa, showed a very similar bacterial compositions in contrast to sputum and bronchial aspirate samples. Thus, sputum and bronchial aspirate samples are upper bronchial tree samples that are not representative of the lower bronchial mucosa flora, and bronchoalveolar lavage samples showed the results closest to those for the bronchial mucosa. Our data confirm that the bronchial tree is not sterile in COPD patients and support the existence a different microbiota in the upper and lower compartments.

Mycoplasma pneumoniae and Streptococcus pneumoniae caused different microbial structure and correlation network in lung microbiota

“…Sputum microbiota was demonstrated to be not concordant to microbes in the lung (13,14), and lung tissue could be collected only when lung transplantation will be conducted (3). This drove BALF sampling to be preferable strategy, in evaluating lung microbiota and corresponding involvement in lung diseases.…”

Single-Molecule Long-Read 16S Sequencing To Characterize the Lung Microbiome from Mechanically Ventilated Patients with Suspected Pneumonia

“…Prior approaches to bacterial identification by DNA sequencing have included fluorescent Sanger sequencing of hundreds of small variable regions of 16S ribosomal amplimer clones (19,20), length heterogeneity (LH) PCR for 16S ribosomal variable regions (21), restriction fragment polymorphisms in 16S (19,21), arrays with bacterium-specific probes, such as PhyloChip (22,23), and early applications of NGS (24,25). These methods have been applied to various clinical situations, such as the microbiome of suboptimally controlled asthma (22), cystic fibrosis (19,21), chronic obstructive pulmonary disease (COPD) (24,26,27), bronchiectasis (28), pleurisy (20), forensic assessment of drowning (25), and intubated patients (23). These studies have revealed unexpectedly large numbers of bacterial genera in patients with clinical illnesses and in healthy individuals (29,30).…”

Genetic determinants of antibiotic resistance in oropharyngeal streptococci in patients with chronic obstructive pulmonary disease and in those with asthma

“…Streptococcus pneumoniae -один из наиболее часто вы-являемых микроорганизмов, идентифицируемых в дыха-тельных путях пациентов с ХОБЛ даже в стабильный пе-риод без эпизодов обострений и антибиотикотерапии за предшествующие 12 мес [1]. D. Garcha и соавт.…”